Examples of quantum mechanical involvement in biological systems

Can anyone can point me to any well established examples of quantum mechanical involvement in biological systems besides photosynthesis, e.g. http://www.lbl.gov/Science-Articles/Archive/PBD-quantum-secrets.html" [Broken]? I've only seen some other (speculative) involving quantum "spin" and bird migration. Hoping to identify more 'hard evidence' examples for an article I'm preparing.
TIA for any help!

As Academic here said, chemistry is essentially quantum-mechanical. Or at least the fundamentals of it, such as chemical bonding and reactivity. So quantum mechanics certainly has an important role in biochemistry. But on the other hand, it is the same role that it has in the rest of chemistry. Photosynthesis, for instance, involves absorption of light by matter - which is a quantum mechanical process, and it also involves things like the transfer of electrons, which is also a quantum mechanical process. But these processes are of course not at all unique to biochemistry, or even chemistry itself, so it's not a surprise, exactly.

If the question is: "Is quantum mechanics significant to biological/biochemical processes in such a way that biochemists need to learn quantum mechanics [more than any other chemist]?"
The answer most in the field would give to that is simply "No."

As it stands right now, biochemists know less quantum stuff than most chemists, (I'm not knocking 'em for it) as they're the farthest removed from these 'fundamentals' where QM is involved, i.e. reactions and bonding and such. They focus rather on the bigger things which are specific to biochemistry, such as protein structure and function, genetics and such. Whereas studying light absorption in photosynthesis (for instance) is better left to physical chemists, chemical physicists, and quantum chemists, who have more detailed knowledge on light-matter interactions in chemistry.

So one must distinguish biochemistry and other diciplines, even though the other diciplines might be studying biochemical systems! The reason why the answer to the question above was 'no' is because once you reach the 'biochemical' level, quantum mechanical effects are no longer in play. E.g. you don't need quantum mechanics to figure out gene regulation, or protein folding, or what a protein does in a cell. But you may need quantum mechanics to fully understand how it does it, but it's the same for any chemical reaction. (and the more you 'zoom in', the more quantum mechanical it becomes)

I've only seen some other (speculative) involving quantum "spin" and bird migration.

This isn't really speculative. Some birds do have magnetoreception, they're pretty sure.
Since cells communicate chemically, you need something that reacts to magnetic fields strongly enough to affect chemistry.
The only thing that could be (given that we haven't found any tiny induction coils in cells) is molecules with a net electronic spin. This is quite unusual, because spin seldom plays such a direct role in chemistry and (equivalently) little chemistry is affected by magnetic fields.

(However there is unfortunately a lot of speculative nonsense out there in this realm. Which is why, even though I do quantum-chemical studies of biochemical systems, I don't use the term 'quantum biology' and don't like it. I think it implies quantum effects of macroscopic significance within bio systems, which is something not generally believed to exist.)

Can anyone can point me to any well established examples of quantum mechanical involvement in biological systems besides photosynthesis, e.g. http://www.lbl.gov/Science-Articles/Archive/PBD-quantum-secrets.html" [Broken]? I've only seen some other (speculative) involving quantum "spin" and bird migration. Hoping to identify more 'hard evidence' examples for an article I'm preparing.
TIA for any help!

There's an open DARPA call for research proposals regarding this exact question:

Haha, indeed!
Looking at their definitions, they seem to define it as quantum effects which are surprising and/or unusual for biological systems, but explicitly not ones which are completely trivial (e.g. the quantum mechanics of chemical bonding). The problem is, you can't really explain this to a layperson. Understanding why some effects are surprising and others not, implicitly requires an in-depth understanding of quantum mechanics, chemistry and how they relate. Unfortunately, the pop-sci press doesn't help much here.

For instance, say it turned out that a current theory on magnetoreception was true, and that it works with the coupled spins of a NADH* - O2*- radical pair. This would be very special and unusual, but hardly impossible, nor at odds with theory. As I said, chemical reactions that depend on magnetic field orientations are not well-known. Because radical reactions are somewhat uncommon, because radicals are not very stable. Because the effect of magnetic fields on them is still very small, and also for purely practical reasons: It's not usual to keep a molecule oriented spatially!

I can imagine how the media could/would spin it (no pun intended). "Scientists believed that magnetic fields couldn't affect chemistry, but biology and quantum mechanics show otherwise!". Evoking images of stuffy conservative professors saying "that's impossible!" (even though nobody ever actually said any such thing) only to be proven wrong by the wonders of evolution. Then you get the journalists pointing to bogus stuff like "quantum consciousness" ideas etc, as if they were suddenly more plausible because of this. Finally the frauds selling magnetic wristbands and whatnot start acting like they've been 'vindicated'.

Well, that's just the http://www.phdcomics.com/comics/archive/phd051809s.gif" [Broken], I suppose.

Adding a bit more reality to the discussion. Howard Hughes Medical Institute’ s Summer ’04 Bulletin, Volume 17, No.2 has an excellent article “Cells Aglow.” Here is a quote from the article:

That special signaling is exactly what happens when the two different colors of GFP [Tsien also engineered the jellyfish green fluorescent protein (GFP)] overlap. In a quantum-mechanical handoff of energy, one GFP absorbs light of a certain wavelength and transfers the energy to the other GFP, which emits light of a different wavelength. So, for instance, light that would ordinarily cause a GFP to glow cyan makes it glow yellow instead. Anything in the biochemistry of a cell that changes the distance between the GFPs, or their relative orientation, sends a conspiracy signal back to headquarters.
http://www.hhmi.org/bulletin/summer2004/tsien/tsien2.html [Broken]

FRET has been around for a while. It's also not a biological phenomenon.

And, the topic is "Examples of quantum mechanical involvement in biological systems." I provided information. Nothing more or less. The article itself is worth reading. Also please note the beginning of the article begins with this statement:

I like pretty colors," Tsien says. His casual comment belies the fact that his artistic sensibilities—combined with shrewd scientific instincts—helped foment a revolution in cell biology and neurobiology."

Andy and Alxm, Howard Hughes Medical Institute's 2009 Annual Report appears to me to be a great resource: Here's a quote though the whole report is awe-inspiring.

Fresh perspective is a precious
commodity in science. And
this year, HHMI identified
50 early career scientists whose
provocative and promising
research holds the potential
to transform our understanding
of biological phenomena—
from how microbial communities
interact to the complex relationships between thousands
of proteins.http://www.hhmi.org/annualreport2009/_files/downloads/HHMI_AR09.pdf

Andy and Alxm, Howard Hughes Medical Institute's 2009 Annual Report appears to me to be a great resource: Here's a quote though the whole report is awe-inspiring.

Fresh perspective is a precious commodity
in science. And this year, HHMI identified
50 early career scientists whose provocative and promising
research holds the potential
to transform our understanding
of biological phenomena—
from how microbial communities
interact to the complex relationships between thousands
of proteins.http://www.hhmi.org/annualreport2009/_files/downloads/HHMI_AR09.pdf

I am cautioning you not to confuse the hype with real science. Real science is much more boring.

Hi Andy, you appear to be referring to Howard Hughes Medical Institute's 2009 Annual Report. I honestly didn’t notice any *hype* in Howard Hughes Medical Institute's 2009 Annual Report. For example: 02 Tsien Receives Nobel Prize
“By co-opting the proteins that make some jellyfish glow, HHMI investigator Roger Y. Tsien and others have provided an invaluable set of tools for visualizing cells and their components. Tsien, a professor at the University of California, San Diego, shared the 2008 Nobel Prize in Chemistry for the discovery and development of green fluorescent proteins (GFPs) with Osamu Shimomura of the Marine Biological Laboratory and Martin Chalfie of Columbia University.”

By the way, I love Science. I don’t consider it to be boring. Do you consider 02 Tsien Recieves Nobel Prize as hype? Do you think an "invaluable set of tools for visualizing cells and their components" is hype? Please tell me what you consider to be hype within the pdf. Also, as noted in the report, "The Howard Hughes Medical Institute is the nation’s largest private supporter of academic biomedical research." Do you consider biomedical research to be hype? You don't think it is 'real science'?

ViewsofMars: That's the fourth post of yours in this thread on HHMI and Roger Tsien, a subject which doesn't really have much at all to do with the topic at all.

Tsien's a fine researcher. I even have a copy of his Nobel poster somewhere. But he's a biochemist, and his work centered on making mutations to GFP to make it usable,
change the colors, etc, essentially by trial-and-error. There was no quantum mechanical theory involved in that work at all.
It's not like QM calculations were done to predict the colors before performing the mutations. (This is almost technically feasible today, but certainly wasn't when he did the work. But even now it'd probably still be faster to just use trial-and-error)

Tsien is actually a chemist (he originally made his name by designing and synthesizing calcium-sensing dye molecules) and he has said in his Nobel lecture that he doesn't know how to perform many of the molecular biology procedures needed to create some of the new GFP variants his lab has designed. However, because of his background as a chemist, he has the insight to be able to look the chemical structure of GFP and be able to think of rational mutations that would change the photophysical properties of GFP, a skill that many biologists do not have.

Certainly, quantum mechanics is useful for many tools in biology research. For example, non-linear optical imaging techniques (e.g. two photon imaging, second-harmonic generation, coherent raman scattering, etc.) all require some knowledge of quantum mechanics to be able to understand how they work. Similarly, magnetic resonance imaging (for imaging large-scale objects) and nuclear magnetic resonance spectroscopy (for studying the shape and dynamics of biological and non-biological molecules) are also deeply based in quantum mechanics. Fluorescence, FRET, GFP, etc. fall into the category of tools used to study biology and not actual biology.

However, while a biologist (or at least biophysicist) might need to understand quantum mechanics in order to implement these techniques, quantum mechanics isn't needed to understand much of the underlying biology.

Biological Systems
ORNL's initiative in complex biological systems engages organizations and disciplines across the Laboratory. In particular, it draws on programs in comparative and functional genomics, structural biology, and computational biology and bioinformatics. This initiative focuses ORNL's distinctive expertise and facilities in in a wide range of biological fields on the challenges of observing and understanding the functioning of complex biological systems.
[Please read on . . .]
http://www.ornl.gov/ornlhome/biological_systems.shtml [Broken]

3. Last of all, I wanted to mention that Jeff Lichtman, professor of molecular biology and cellular biology at Harvard states, “The strength of inductive science, however is that new observational tools often reveal unexpected things that force you to confront the disconnect between the current worldview and the revealed world . . . especially when you have young colleagues who bring fewer bias to biological phenomena. Microscopes are particularly valuable tools for this endeavor in neurobiology because they are a direct link between cell-biological phenomena and the visual system, our most sophisticated sensory mechanism. (Closely Watched Organisms by Jeff Lichtman , HHMI Bulletin, February 2006 http://www.hhmi.org/bulletin/feb2006/pdf/Organisms.pdf [Broken] ) Excellent article!

However, because of his background as a chemist, he has the insight to be able to look the chemical structure of GFP and be able to think of rational mutations that would change the photophysical properties of GFP, a skill that many biologists do not have.

You could use 'chemical intuition' but having read the paper once, as far as I recall it was basically trial-and-error in this specific case, and some luck; Not that there's anything wrong with that. All scientific discovery is part luck.

[..]Fluorescence, FRET, GFP, etc. fall into the category of tools used to study biology and not actual biology. However, while a biologist (or at least biophysicist) might need to understand quantum mechanics in order to implement these techniques, quantum mechanics isn't needed to understand much of the underlying biology.

Certainly. But you don't necessarily have to know how the tools work to use them, and in the cases where you do, it tends to be done by the specialists on those tools, rather than specialists on the systems in question. E.g. in my case, quantum chemical methods, which in general haven't quite reached the 'black box' level where they can be used without intimate knowledge of how they work.

GFP on the other hand is itself an excellent 'black box'. The biochemist doesn't need to know how or why the fluorescence works, just that it fluoresces. Stick the gene in and you get a fluorescent protein. (I'm pretty sure Tsien's being modest and probably knows how to do that much. One of our undergrad courses has a project of putting GFP into E Coli, so even though I don't know how to do it myself, it'd seem to be pretty routine for biochemists)

Tsien's a fine researcher. I even have a copy of his Nobel poster somewhere. But he's a biochemist, and his work centered on making mutations to GFP to make it usable, change the colors, etc, essentially by trial-and-error.

I'm not 100% sure about the trial and error. Some added information about Roger Tsien, Ph.D:

University of California, San Diego Professor Roger Tsien, Ph.D.,

Education: B.S., chemistry and physics, Harvard College
Ph.D., physiology, University of Cambridge, England

Appointments: Professor of Pharmacology, UC San Diego School of Medicine

Professor of Chemistry and Biochemistry, UC San Diego

Howard Hughes Medical Institute Investigator (1989 -
present)

Memberships:
National Academy of Sciences
Institute of Medicine
European Molecular Biology Organization

Tsien, a professor of pharmacology, chemistry and biochemistry at UC San Diego and a Howard Hughes Medical Institute investigator.

2.

Tsien attended Harvard College on a National Merit Scholarship, graduating at age 20 with a degree in chemistry and physics. He received his doctorate degree at the University of Cambridge where he was a Marshall Scholar. As a graduate student at Cambridge, he developed molecules to track and control the levels of calcium inside cells, levels that play a major role in the regulation of nerve impulses, muscle contraction, and fertilization.

3.

After postdoctoral work at Cambridge, he moved to the University of California, Berkeley, where he rose to professor of physiology. He moved to UC San Diego in 1989.

Also, just so people don't get confused between Professor Roger Tsien and Professor Robert Tjian. My post #16 regarding Robert Tjian was in reference to my post #11 pertaining to Howard Hughes Medical Institute's 2009 Annual Report wherein the pdf he was mentioned. Basically, I vis a vis’d him into our conversation. HA, HA, HA, LOL! I love Howard Hughes Medical Institute just as much as I love NASA!

Then read the research papers instead of instead of continuing to fill this thread with irrelevant and unrelated trivia. You're disputing something I'd read in their paper by citing his CV? In what way would that be relevant? You don't think that important discoveries are made through luck? Or that I implied Tsien is somehow a lesser scientist because of it?

To test the hypothesis that Ser 65 undergoes additional dehydration to form a vinyl side chain, we mutated that residue [..] Serendipitously, all four mutants showed single excitation peaks, located at 470-490 nm, whose amplitudes were four- to sixfold greater than that of wild-type [..] These results exclude vinyl formation. [..] The crucial post-translational oxidation to produce the fluorophore from the nascent polypeptide chain proceeded about fourfold more rapidly in S65T. This acceleration ameliorates a potentially significant limitation in using GFP as a reporter protein for rapid gene inductions.

- "Improved Green Fluorescence", Nature, v373 (1995), p663.

So you're right. It wasn't trial-and-error. They were in fact studying a completely different aspect of the function at the time.

Then read the research papers instead of instead of continuing to fill this thread with irrelevant and unrelated trivia. You're disputing something I'd read in their paper by citing his CV? In what way would that be relevant? You don't think that important discoveries are made through luck? Or that I implied Tsien is somehow a lesser scientist because of it?

- "Improved Green Fluorescence", Nature, v373 (1995), p663.

So you're right. It wasn't trial-and-error. They were in fact studying a completely different aspect of the function at the time.

I just located the papers! I haven't read them. And by the way, you are the one Alxm by replying to Ygggdrasil, it is you who keeps bringing Roger Tsien up. And you failed to provide adequate information about Roger Tsien. You give people the impression he is *just* a biochemist. Tsien is not just a biochemist! It's very important to me to protect scientists that have an outstanding reputation such as Tsien does have.

Bye the way, my contribution in post #16 pertaining to "Biological Systems" is worthy of notation. I'll pat myself on the back. Thank you very much. Good day.
Mars